title: Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML.
abstract: The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain.
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom;
authors.forename: Fawaz
authors.initials: F
authors.lastname: Ghali
authors.forename: Ritesh
authors.initials: R
authors.lastname: Krishna
authors.forename: Pieter
authors.initials: P
authors.lastname: Lukasse
authors.forename: Salvador
authors.initials: S
authors.lastname: Martínez-Bartolomé
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
mesh_terms: D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000592:standards / Q000706:statistics & numerical data*; D057386:Search Engine; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins